Novel polyelectrolyte multilayer (PEM) coatings for enhanced protein separations in open tubular CEC (OT-CEC) are reported. Use of four cationic polymers (poly-L-lysine, poly-L-ornithine, poly-L-lysine-serine, and poly-L-glutamic acid-lysine), and three anionic molecular micelles, sodium poly(N-undecanoyl-L-leucyl-alaninate) (poly-L-SULA), sodium poly(N-undecanoyl-L-leucyl-valinate) (poly-L-SULV), and sodium poly(undecylenic sulfate) (poly-SUS) were investigated in PEM coatings for protein separations. The simultaneous effects of cationic polymer concentration, number of bilayers, temperature, applied voltage, and pH of the BGE on the separation of four basic proteins (alpha-chymotrypsinogen A, lysozyme, ribonuclease A, and cytochrome c) were analyzed using a Box Behnken experimental design. The influence of NaCl on the run-to-run reproducibility was investigated for PEM coatings containing each cationic polymer. All coatings exhibited excellent reproducibilities with a %RSD of the EOF less than 1% in the presence of NaCl. Optimal conditions were dependent on both the cationic and anionic polymers used in the PEM coatings. poly-L-glutamic acid-lysine produced the highest resolution and longest migration time. The use of molecular micelles to form PEM coatings resulted in better separations than single cationic coatings. Chiral poly-L-SULA and poly-L-SULV resulted in higher protein resolutions as compared to the achiral, poly-SUS. Furthermore, the use of poly-L-SULV reversed the elution order of lysozyme and cytochrome c when compared to poly-L-SULA and poly-SUS.